Contacts of the helix formed by residues 546 - 559 (chain G) in PDB entry 1O1F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 546 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544G LYS 4.6 3.5 + - - -
545G ALA* 1.3 78.1 + - - +
547G ASP* 1.3 80.2 + - + +
548G THR* 3.0 28.0 - - - +
549G SER* 2.9 17.4 + - - -
550G PHE* 2.8 23.7 + - - +
596G LEU* 3.5 7.6 - - - +
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Residues in contact with ASP 547 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546G THR* 1.3 77.7 - - + +
548G THR* 1.3 54.4 + - - +
550G PHE* 3.0 13.1 - - - +
551G MLY 2.7 36.0 + - - +
592G ILE* 3.7 17.0 - - - +
593G SER* 3.3 9.0 - - - -
594G GLY* 2.9 29.2 + - - -
595G TRP* 4.5 0.6 - - - +
596G LEU* 3.4 31.8 + - - +
597G GLU 4.9 0.2 + - - -
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Residues in contact with THR 548 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478 MET* 2.9 5.7 - - - +
546G THR* 3.0 17.6 - - + +
547G ASP* 1.3 79.4 - - - +
549G SER* 1.3 62.3 + - - +
551G MLY 3.3 29.1 + - - +
552G ASN* 2.8 36.9 + - - +
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Residues in contact with SER 549 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458 VAL* 2.4 21.6 - - - +
468 GLY* 2.2 31.9 - - - +
478 MET* 2.6 8.5 + - - +
539G GLU* 2.8 24.2 + - - +
545G ALA* 4.2 2.0 - - - -
546G THR* 2.9 31.2 + - - -
548G THR* 1.3 84.9 - - - +
550G PHE* 1.3 65.4 + - - +
552G ASN 3.0 0.9 + - - -
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Residues in contact with PHE 550 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468 GLY* 1.1 62.6 - - - +
532G ILE* 4.4 3.6 - - + -
535G ILE* 3.9 20.9 - - + -
536G LEU* 3.2 55.0 - - + -
539G GLU* 4.1 3.4 - - + -
546G THR 2.8 9.5 + - - +
547G ASP* 3.0 8.5 - - + +
549G SER* 1.3 73.3 + - - +
551G MLY 1.3 52.5 + - - +
553G MLY 3.5 0.2 - - - +
554G LEU* 2.9 30.1 + - + +
592G ILE* 3.0 40.2 - - + -
595G TRP* 4.1 16.2 - + + -
596G LEU* 3.8 18.4 - - + -
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Residues in contact with MLY 551 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468 GLY 2.5 9.7 - - - +
547G ASP 2.7 19.2 + - - +
548G THR* 3.5 31.1 + - - +
549G SER 3.1 0.2 - - - -
550G PHE* 1.3 72.5 + - - +
552G ASN* 1.3 69.8 + - - +
554G LEU* 2.7 27.6 + - + +
555G TYR* 3.0 42.2 + - + +
576G GLU* 5.3 5.4 - - - -
577G ALA* 5.0 2.5 - - - -
578G HIS* 3.8 34.3 - - + +
592G ILE* 4.4 18.6 - - + -
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Residues in contact with ASN 552 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448 MET* 4.6 1.8 - - + -
468 GLY 2.7 2.2 + - - -
478 MET* 0.8 424.6 - - + +
488 GLY 1.2 52.8 + - - -
508 LYS* 5.9 4.0 - - - +
538 TYR* 6.0 1.6 - - - +
578 GLU* 5.2 9.3 + - - +
548G THR* 2.8 25.7 + - - +
551G MLY 1.3 82.0 + - - -
553G MLY 1.3 7.2 - - - -
555G TYR* 2.9 5.3 + - - -
556G ASP 2.9 1.2 + - - -
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Residues in contact with MLY 553 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1676 GLU 5.2 2.7 - - - -
1686 GLY* 6.4 0.2 - - - -
3556 MET* 5.5 2.0 - - - -
438 VAL* 4.2 17.9 - - + -
448 MET 2.2 27.4 - - - +
458 VAL* 1.1 85.8 - - - +
468 GLY* 1.6 58.3 + - - +
478 MET* 0.9 148.2 + - - +
488 GLY* 2.5 12.6 + - - -
535G ILE* 3.9 17.6 - - + +
538G GLU* 4.3 15.9 - - - +
539G GLU* 3.0 11.9 + - - +
542G PHE* 3.3 33.4 - - - -
550G PHE 3.5 0.2 - - - +
552G ASN 1.3 6.9 - - - -
554G LEU* 1.3 53.0 + - - +
557G GLU* 3.6 11.1 + - - +
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Residues in contact with LEU 554 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468 GLY 2.5 7.7 + - - -
532G ILE* 4.1 22.9 - - + -
535G ILE* 3.4 37.2 - - + -
550G PHE* 2.9 33.5 + - + +
551G MLY 2.8 15.3 - - + +
553G MLY 1.3 75.2 + - - +
555G TYR* 1.3 61.1 + - + +
558G HIS* 3.1 30.4 + - + +
565G PHE* 4.1 16.9 - - + -
579G PHE* 3.9 31.2 - - + -
592G ILE* 4.4 5.6 - - + -
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Residues in contact with TYR 555 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478 MET* 4.2 1.6 - - + -
488 GLY* 2.3 15.7 - - - +
498 GLN 3.4 2.8 - - - +
508 LYS* 5.3 7.0 - - + -
551G MLY 3.0 52.8 + - + +
552G ASN* 2.9 11.3 + - - +
554G LEU* 1.3 71.3 - - + +
556G ASP* 1.3 57.6 + - - +
557G GLU 2.7 12.6 + - - -
559G LEU* 2.7 61.1 + - + +
565G PHE* 3.8 17.7 - + - -
567G LYS* 4.4 12.6 - - + +
568G PRO* 4.5 4.3 - - - +
578G HIS* 2.9 30.9 + - - -
579G PHE* 4.9 0.4 - - + -
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Residues in contact with ASP 556 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428 GLY 4.4 1.6 - - - +
438 VAL* 3.5 14.0 - - + -
448 MET* 3.6 19.4 + - - +
478 MET* 3.5 11.8 - - - +
488 GLY* 0.9 201.4 + - - +
498 GLN* 1.0 141.3 - - - +
508 LYS* 2.7 36.5 + - - +
538 TYR* 4.1 8.9 + - - -
552G ASN 3.6 4.4 - - - +
555G TYR* 1.3 68.1 - - - +
557G GLU* 1.3 45.1 + - - -
559G LEU 5.0 1.0 - - - +
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Residues in contact with GLU 557 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438 VAL* 4.9 9.3 - - + +
478 MET 4.9 0.2 - - - +
488 GLY* 2.1 19.7 - - - -
498 GLN* 2.0 8.9 - - - +
530G MET* 3.6 39.4 - - - +
535G ILE* 4.2 5.6 - - + -
553G MLY 3.6 14.4 - - - +
554G LEU 4.2 0.7 - - - +
555G TYR 2.7 0.4 + - - -
556G ASP 1.3 69.6 - - - -
558G HIS* 1.3 83.6 + - + +
559G LEU 5.2 0.2 - - - -
561G LYS* 4.2 31.8 + - - +
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Residues in contact with HIS 558 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525G LEU* 3.6 24.5 - - + +
530G MET* 2.7 30.9 + - + -
531G GLY* 3.6 16.8 - - - -
532G ILE* 4.1 6.5 + - + -
535G ILE* 3.8 8.5 - - + +
554G LEU* 3.1 26.9 + - + +
555G TYR 2.7 5.5 + - - -
557G GLU* 1.3 90.2 + - + +
559G LEU* 1.3 65.1 + - - +
560G GLY 3.3 0.2 + - - -
561G LYS* 3.1 2.6 + - - -
562G SER* 2.8 39.6 + - - +
565G PHE* 3.7 25.0 - + + -
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Residues in contact with LEU 559 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498 GLN 4.3 10.1 - - - +
518 ASP* 5.7 4.7 - - - +
555G TYR* 2.7 52.7 + - + +
556G ASP 5.0 1.6 - - - +
558G HIS* 1.3 73.0 - - - +
560G GLY* 1.3 68.2 + - - +
561G LYS* 3.0 8.2 + - - +
565G PHE* 3.6 20.4 - - + +
566G GLN* 5.1 0.9 - - - -
567G LYS* 4.2 34.3 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il